1 Code and verbatim

1.1 Syntax highlighting

Here is a sample code chunk, just to show that syntax highlighting works as expected.

not_null <- function (v) {
  if (!is.null(v)) return(paste(v, "not null"))
}

R output is typically shown in the monospace font (here an example with the mtcars dataset in the subfolder data/):

# Import dataset from the data/ folder
mtcars <- read.csv("data/mtcars.csv")
summary(mtcars[,1:4])
##       mpg             cyl             disp             hp       
##  Min.   :10.40   Min.   :4.000   Min.   : 71.1   Min.   : 52.0  
##  1st Qu.:15.43   1st Qu.:4.000   1st Qu.:120.8   1st Qu.: 96.5  
##  Median :19.20   Median :6.000   Median :196.3   Median :123.0  
##  Mean   :20.09   Mean   :6.188   Mean   :230.7   Mean   :146.7  
##  3rd Qu.:22.80   3rd Qu.:8.000   3rd Qu.:326.0   3rd Qu.:180.0  
##  Max.   :33.90   Max.   :8.000   Max.   :472.0   Max.   :335.0

1.2 Verbatim

Here is the structure of the iris dataset.

str(iris)
## 'data.frame':    150 obs. of  5 variables:
##  $ Sepal.Length: num  5.1 4.9 4.7 4.6 5 5.4 4.6 5 4.4 4.9 ...
##  $ Sepal.Width : num  3.5 3 3.2 3.1 3.6 3.9 3.4 3.4 2.9 3.1 ...
##  $ Petal.Length: num  1.4 1.4 1.3 1.5 1.4 1.7 1.4 1.5 1.4 1.5 ...
##  $ Petal.Width : num  0.2 0.2 0.2 0.2 0.2 0.4 0.3 0.2 0.2 0.1 ...
##  $ Species     : Factor w/ 3 levels "setosa","versicolor",..: 1 1 1 1 1 1 1 1 1 1 ...

1.3 Mathjax

A little math formula :

\[x = \sum_{i=1}^{n} \sqrt{\frac{y}{i}} \]

1.4 Cross-referencing

This is an example of crossreferencing figures and tables: reference to figure 4.1, reference to table 2.1.

Please note that in this template only the automatic numbering works, not the hyperlink!

2 Tables

Here is a sample table output.

tab <- aggregate(. ~ Species, data = iris, mean)
kable(tab,
  caption = "Species-specific mean lengths and widths.")
Table 2.1: Species-specific mean lengths and widths.
Species Sepal.Length Sepal.Width Petal.Length Petal.Width
setosa 5.006 3.428 1.462 0.246
versicolor 5.936 2.770 4.260 1.326
virginica 6.588 2.974 5.552 2.026

3 Tabbed sections

Comparison between the classical tabs and the pill tabs:

3.1 Classical tabs

Classical tabs without fading effect.

3.1.1 First tab

Quisquam sunt fugit sed aut quis et rerum mollitia. Qui consectetur eius autem ut assumenda alias. Repudiandae aut deleniti quod saepe nihil ratione alias laborum. Quibusdam aspernatur autem omnis voluptatum. Delectus illo non aut. Perferendis sunt facilis sed quam velit. Veniam voluptates ut adipisci vel debitis deserunt rerum exercitationem. Accusamus quod eius occaecati voluptatem. Ut et qui veritatis. Nulla non eum id consectetur autem pariatur. Labore aperiam officiis molestiae sed ut perferendis ea. Aperiam aut ratione autem dolorem. Fuga reprehenderit tempora ut ipsam cumque officiis dolorum. Sapiente omnis rerum sint quibusdam et delectus ratione. Molestiae praesentium rerum debitis deleniti voluptates enim. Nihil aperiam velit provident accusamus suscipit voluptates. Aut sequi id debitis tempore. Qui atque quas sed illum officia maiores incidunt. Similique maxime aliquam corrupti aut provident eaque. Laudantium placeat cupiditate pariatur dolore perspiciatis expedita impedit nobis. Quaerat non temporibus tempora provident eligendi.

3.1.2 Second tab

Cum eaque dicta architecto culpa eius. Dignissimos officiis error exercitationem. Adipisci odit ad ea iusto fugiat laborum maiores. Dolore sunt et veritatis alias nesciunt maxime cumque. Culpa aut non ea. Culpa ex quia debitis sint eveniet cum. Non eos ex aperiam dolor hic. Consectetur delectus placeat rerum consequuntur ducimus sed fugiat non. Aut voluptatem et et. Omnis sunt veniam omnis ullam. Dolorem eius perspiciatis et veniam hic reprehenderit ipsam ut. Exercitationem rem eius quo. Nemo quis in voluptatibus ex. Aut nihil quo iure quia. Error quam quidem inventore. Aut est est aut atque ipsum aut repellat. Eligendi delectus aut et quia voluptas dolores. Perspiciatis et reiciendis deleniti harum nihil officiis aperiam. Laborum necessitatibus beatae modi aut illo. Quaerat esse eum ipsa quisquam totam. Vitae nesciunt excepturi voluptate iusto molestiae qui animi corrupti. Voluptates et illum quia.

3.2 Pill tabs

Pill tabs with fading effect.

3.2.1 First tab

Quisquam sunt fugit sed aut quis et rerum mollitia. Qui consectetur eius autem ut assumenda alias. Repudiandae aut deleniti quod saepe nihil ratione alias laborum. Quibusdam aspernatur autem omnis voluptatum. Delectus illo non aut. Perferendis sunt facilis sed quam velit. Veniam voluptates ut adipisci vel debitis deserunt rerum exercitationem. Accusamus quod eius occaecati voluptatem. Ut et qui veritatis. Nulla non eum id consectetur autem pariatur. Labore aperiam officiis molestiae sed ut perferendis ea. Aperiam aut ratione autem dolorem. Fuga reprehenderit tempora ut ipsam cumque officiis dolorum. Sapiente omnis rerum sint quibusdam et delectus ratione. Molestiae praesentium rerum debitis deleniti voluptates enim. Nihil aperiam velit provident accusamus suscipit voluptates. Aut sequi id debitis tempore. Qui atque quas sed illum officia maiores incidunt. Similique maxime aliquam corrupti aut provident eaque. Laudantium placeat cupiditate pariatur dolore perspiciatis expedita impedit nobis. Quaerat non temporibus tempora provident eligendi.

3.2.2 Second tab

Cum eaque dicta architecto culpa eius. Dignissimos officiis error exercitationem. Adipisci odit ad ea iusto fugiat laborum maiores. Dolore sunt et veritatis alias nesciunt maxime cumque. Culpa aut non ea. Culpa ex quia debitis sint eveniet cum. Non eos ex aperiam dolor hic. Consectetur delectus placeat rerum consequuntur ducimus sed fugiat non. Aut voluptatem et et. Omnis sunt veniam omnis ullam. Dolorem eius perspiciatis et veniam hic reprehenderit ipsam ut. Exercitationem rem eius quo. Nemo quis in voluptatibus ex. Aut nihil quo iure quia. Error quam quidem inventore. Aut est est aut atque ipsum aut repellat. Eligendi delectus aut et quia voluptas dolores. Perspiciatis et reiciendis deleniti harum nihil officiis aperiam. Laborum necessitatibus beatae modi aut illo. Quaerat esse eum ipsa quisquam totam. Vitae nesciunt excepturi voluptate iusto molestiae qui animi corrupti. Voluptates et illum quia.

4 Figures

4.1 Base graphics

A base graphics histogram:

hist(rnorm(100))
A Histogram made with the basic graphics package

Figure 4.1: A Histogram made with the basic graphics package

5 Interactive figures with plotly

If the package ‘plotly’ is installed, the following code block will be executed:

# If plotly is installed run:
p <- plotly::plot_ly(data = mtcars, x = ~mpg, y = ~wt, color = ~cyl)
plotly::add_markers(p)

Figure 5.1: This is the interactive htmlwidget ‘plotly’

6 Bibliography

Link a .bib document via the YAML header, and the bibliography will be printed at the very end (as usual). The default bibliography style is provided in the sage-harvard.csl file (do not delete), which adopts the SAGE Harvard reference style.

References can be cited directly within the document using the R Markdown equivalent of the citation system [@key], where key is the citation key in the first line of the entry in the .bib file. Example: (Taylor and Green, 1937). To cite multiple entries, separate the keys by semicolons, e.g. (Kamm, 2000; Knupp, 1999).

There is also the package citr, which I highly recommend: citr provides functions and an RStudio add-in to search a BibTeX-file to create and insert formatted Markdown citations into the current document. If you are using the reference manager Zotero the add-in can access your reference database directly.

6.1 Software

If you want to include a paragraph on the software used, here is some example text/code to get the current R and package versions. The code to generate a bibliography file including all package references has been already added at the beginning of this script (code chunk ‘generate-package-refs’).

All analyses were performed using the statistical software R (version 4.1.2) (R Core Team, 2021). This report, including tables and figures, was generated using the packages ‘rmarkdown’ (version 2.14) (Allaire et al., 2022), and ‘knitr’ (version 1.39) (Xie, 2022).

6.2 References

Allaire J, Xie Y, McPherson J, et al. (2022) Rmarkdown: Dynamic Documents for r. Available at: https://CRAN.R-project.org/package=rmarkdown.
Kamm J (2000) Evaluation of the Sedov-von Neumann-Taylor blast wave solution. Technical Report LA-UR-00-6055. Los Alamos National Laboratory.
Knupp P (1999) Winslow smoothing on two-dimensional unstructured meshes. Eng Comput 15: 263–268.
R Core Team (2021) R: A Language and Environment for Statistical Computing. Vienna, Austria: R Foundation for Statistical Computing. Available at: https://www.R-project.org/.
Taylor G and Green A (1937) Mechanism of the production of small eddies from large ones. P Roy Soc Lond A Mat 158(895): 499–521.
Xie Y (2022) Knitr: A General-Purpose Package for Dynamic Report Generation in r. Available at: https://yihui.org/knitr/.